a9664d23dd1b814c2a3c6dad625fb3362368c4b8
galt
  Mon Aug 12 16:48:35 2019 -0700
Tolerate the name mismatch for .2bit files used with hgPcr GencodeGenes

diff --git src/hg/utils/blatServersCheck/blatServersCheck.c src/hg/utils/blatServersCheck/blatServersCheck.c
index fce79e2..29ade64 100644
--- src/hg/utils/blatServersCheck/blatServersCheck.c
+++ src/hg/utils/blatServersCheck/blatServersCheck.c
@@ -1,315 +1,316 @@
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 
 /* blatServersCheck - Check that the blatServers table value match the 
  * actual running gfServers.
  */
 
 #include "common.h"
 #include "options.h"
 #include "jksql.h"
 #include "hgConfig.h"
 #include "genoFind.h"
 #include "net.h"
 #include "hash.h"
 #include "obscure.h"
 
 char *database = NULL;
 char *host     = NULL;
 char *user     = NULL;
 char *password = NULL;
 
 struct sqlConnection *conn = NULL;
 
 char *blatServersTableName = "blatServers";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "blatServersCheck - Check the blatServers table matches running gfServers\n"
   "usage:\n"
   "   blatServersCheck profile\n"
   "profile should be from hg.conf like central or rrcentral\n"
   "options:\n"
   " -verbose=2  can show details for each server.\n"
   "\n"
 // TODO copied from another progrma, not sure it still works here.
 //  "Use the HGDB_CONF environment variable to specify which configuration to use, for example\n"
 //  "HGDB_CONF=/usr/local/apache/cgi-bin/hg.conf\n"
   );
 }
 
 
 static struct optionSpec options[] = {
 /*
    {"chunkSize", OPTION_INT},
    {"chunkWait", OPTION_INT},
    {"squealSize", OPTION_INT},
    {"purgeStart", OPTION_INT},
    {"purgeEnd", OPTION_INT},
    {"purgeTable", OPTION_STRING},
    {"dryRun", OPTION_STRING},
 */
    {"-help", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 char *getCfgOption(char *config, char *setting)
 /* get setting for specified config */
 {
 char temp[256];
 safef(temp, sizeof(temp), "%s.%s", config, setting);
 char *value = cfgOption(temp);
 if (!value)
     errAbort("setting %s not found!",temp);
 return value;
 }
 
 int statusServer(char *hostName, char *portName, boolean isTrans, struct hash *versionHash)
 /* Send status message to server arnd report result.
  * Returns -1 for connection error.
  * Returns -2 for error reading string.
  * Returns -3 for type mismatch.
  * Returns -4 for host mismatch.
  * Returns -5 for port mismatch.
  */
 {
 char buf[256];
 int sd = 0;
 int ret = 0;
 
 /* Put together command. */
 sd = gfMayConnect(hostName, portName);
 if (sd == -1)
     {
     warn("Error connecting to %s:%s",  hostName, portName);
     return -1;
     }
 
 sprintf(buf, "%sstatus", gfSignature());
 mustWriteFd(sd, buf, strlen(buf));
 
 for (;;)
     {
     if (netGetString(sd, buf) == NULL)
         {
         warn("Error reading status information from %s:%s",  hostName, portName);
         ret = -2;  // error reading response
         break;
         }
     if (sameString(buf, "end"))
 	{
         break;
 	}
     else
 	{
 	verbose(2, "%s\n", buf);
         if (startsWith("version ", buf))
 	    {
 	    char *hashKey = buf+strlen("version ");
 	    hashIncInt(versionHash, hashKey);   // count how many with this version
 	    }
         if (startsWith("type ", buf))
 	    {	    
 	    if (sameString(buf, "type translated") && !isTrans)
 		{
 		warn("type mismatch: gfServer says type translated but db says isTrans==0");
 		ret = -3;  // type mismatch
 		break;
 		}
 	    if (sameString(buf, "type nucleotide") && isTrans)
 		{
 		warn("type mismatch: gfServer says type nucleotide but db says isTrans==1");
 		ret = -3;  // type mismatch
 		break;
 		}
 	    }
         if (startsWith("host ", buf))
 	    {
 	    if (!sameString(buf+strlen("host "), hostName))
 		{
 		warn("host mismatch: gfServer says %s but db says db=%s", buf, hostName);
 		ret = -4;  // host mismatch
 		break;
 		}
 	    }
         if (startsWith("port ", buf))
 	    {
 	    if (!sameString(buf+strlen("port "), portName))
 		{
 		warn("port mismatch: gfServer says %s but db says port=%s", buf, portName);
 		ret = -5;  // port mismatch  // probably never happens.
 		break;
 		}
 	    }
 	}
     }
 close(sd);
 return(ret);
 }
 
 
 int getFileList(char *hostName, char *portName, char *db)
 /* Get and display input file list. */
 {
 char buf[256];
 int sd = 0;
 int fileCount;
 int i;
 int ret = 0;
 char twoBitName[256];
 
 safef(twoBitName, sizeof twoBitName, "%s.2bit", db);
 
 /* Put together command. */
 sd = netMustConnectTo(hostName, portName);
 sprintf(buf, "%sfiles", gfSignature());
 mustWriteFd(sd, buf, strlen(buf));
 
 /* Get count of files, and then each file name. */
 if (netGetString(sd, buf) != NULL)
     {
     fileCount = atoi(buf);
     for (i=0; i<fileCount; ++i) // could have multiples if .nib used?
 	{
 	char *fileName = netRecieveString(sd, buf);
 	//printf("%s\n", fileName);
 	verbose(2, "%s\n", fileName);
-	if (!endsWith(fileName,".nib"))
+	// if .nib or Kg genes for isPcr, cannot confirm the name.
+	if (!endsWith(fileName,".nib") && !strstr(db, "Kg"))  
 	    {
 	    if (!sameString(fileName, twoBitName))
 		{
 		warn("2bit name mismatch fileName=%s twoBitName=%s", fileName, twoBitName);
 		ret = -1;  // 2bit name mismatch
 		break;
 		}
 	    }
 	}
     }
 close(sd);
 return ret;
 }
 
 
 void blatServersCheck(char *config)
 /* Check blatServers table against running gfServers */
 {
 
 struct hash *hash = hashNew(12);
 struct hash *versionHash = hashNew(6);
 
 char hashKey[256];
 
 /* get connection info */
 database = getCfgOption(config, "db"      );
 host     = getCfgOption(config, "host"    );
 user     = getCfgOption(config, "user"    );
 password = getCfgOption(config, "password");
 
 conn = sqlConnectRemote(host, user, password, database);
 
 struct sqlResult *sr;
 char **row;
 char query[256];
 int totalRows = 0;
 
 verbose(1, "-------------------\n");
 verbose(1, "Reading table %s\n", blatServersTableName);
 
 
 totalRows = sqlTableSize(conn, blatServersTableName);
 verbose(1,"totalRows=%d\n", totalRows);
 
 if (totalRows==0)
     {
     errAbort("table %s is empty!", blatServersTableName);
     }
 
 int errCount = 0;
 
 sqlSafef(query,sizeof(query), "select db, host, port, isTrans from %s", blatServersTableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *db      = row[0];
     char *host    = row[1];
     char *portStr = row[2];
     unsigned int port  = sqlUnsigned(portStr);
     unsigned int trans = sqlUnsigned(row[3]);
     boolean isTrans = (trans == 1);
 
     int res = statusServer(host, portStr, isTrans, versionHash);
     int res2 = 0;
     if (res != -1)  // if not a connection error, proceed.
 	{
 	res2 = getFileList(host, portStr, db);
 	}
     safef(hashKey, sizeof hashKey, "%s:%s", host, portStr);
     struct hashEl *hel = hashLookup(hash, hashKey);
     if (hel == NULL)
 	{
 	hashAdd(hash, hashKey, NULL);
 	}
     else
 	{
 	warn("duplicate host:port %s found", hashKey);
 	}
 
     if ((res != 0) || (res2 != 0) || (hel != NULL))
 	{
 	++errCount;
     	verbose(1, "db=%s host=%s port=%d isTrans=%d res=%d res2=%d\n\n", db, host, port, trans, res, res2);
 	}
     else
 	{
     	verbose(2, "db=%s host=%s port=%d isTrans=%d res=%d res2=%d\n\n", db, host, port, trans, res, res2);
 	}
     }
 
 
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 
 // Show a count of how many servers were of each gfServer version
 struct hashEl *el, *list = hashElListHash(versionHash);
 slSort(&list, hashElCmp);
 verbose(1, "version count\n");
 verbose(1, "-------------\n");
 for (el = list; el != NULL; el = el->next)
    {
    verbose(1, "%s %d\n", el->name, ptToInt(el->val));
    }
 hashElFreeList(&list);
 
 for (el = list; el != NULL; el = el->next)
    {
    verbose(1, "%s %d\n", el->name, ptToInt(el->val));
    }
 hashElFreeList(&list);
 verbose(1, "\n");
 
 if (errCount > 0)
     errAbort("error count=%d", errCount);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 
 if ((argc != 2) || optionExists("-help"))
     usage();
 
 //char *hgdbConf = getenv("HGDB_CONF");
 //if (hgdbConf)
 //    printf("\nHGDB_CONF = %s\n\n", hgdbConf);
 
 blatServersCheck(argv[1]);
 
 printf("No errors found!\n");
 
 return 0;  
 }